geneSubsets-class: geneSubsets: A class to handle the sizes of gene susbets to...

In Rmagpie: MicroArray Gene-expression-based Program In Error rate estimation

Description

Forward gene selection is usually a computationally expensive task. To reduce the computation expense one may want to do not consider one gene at a time but chunks of genes. This class store the sizes of gene susbets to be tested during forward gene selection.

Creating objects

new("geneSubsets", optionValues)

Create a geneSubsets, the sizes of the different subsets are determined by optionValues. The size of the biggest subset maxSubsetSize and the number of subsets to be tried noOfOptions are automatically deducted. The speed is set to high is there are less models than the size of the biggest subset and 'slow' if not.

new("geneSubsets", maxSubsetSize, speed="high")

Create a geneSubsets, with a biggest subset of size maxSubsetSize. If the speed is high the sizes of the subsets are increased by a power of 2 from 1 to the biggest power of 2 smaller than maxSubsetSize. If the speed is slow the sizes of the subsets are increased by 1 from 1 to the maxSubsetSize.

Slots

maxSubsetSize:

numeric. Size of the biggest subset

optionValues:

numeric (vector). Sizes of the subsets in acsending order

noOfOptions:

numeric. Total number of subsets to be tried during backward gene selection

speed:

character. Speed of the backward feature selection. high if the number of models is smaller than the size of the biggest subset, slow if not.

Methods

getMaxSubsetSize(geneSubsets), getMaxSubsetSize(geneSubsets)<-

Retreive and modify the size of the biggest subset (slot maxSubsetSize)

getOptionValues(geneSubsets), getOptionValues(geneSubsets)<-

Retreive and modify the sizes of the subsets of features (slot optionValues)

getNoOfOptions(geneSubsets)

Retreive the total number of subsets to be tried during backward gene selection (slot noModels)

getSpeed(geneSubsets), getSpeed(geneSubsets)<-

Retreive and modify the speed of the backward feature selection. (slot speed)

Author(s)

Camille Maumet

See Also

thresholds,assessment

Examples

geneSubset235 <- new("geneSubsets", optionValues=c(2,3,5))
geneSubset235
getSubsetsSizes(geneSubset235)
getSpeed(geneSubset235)
getMaxSubsetSize(geneSubset235)

geneSubsetMax60 <- new("geneSubsets", maxSubsetSize=60, speed="slow")
geneSubsetMax60

geneSubsetSlow <- new("geneSubsets", maxSubsetSize=70, speed="slow")
geneSubsetSlow

getMaxSubsetSize(geneSubsetMax60) <- 70
geneSubsetMax60

newSizes <- c(1,2,3,4,5)
getSubsetsSizes(geneSubsetMax60) <- newSizes
geneSubsetMax60

getSpeed(geneSubset235) <- 'slow'
geneSubset235

Rmagpie documentation built on Nov. 8, 2020, 11:09 p.m.